Clustal Omega 1.2.4
pair_dist.h
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1/*********************************************************************
2 * Clustal Omega - Multiple sequence alignment
3 *
4 * Copyright (C) 2010 University College Dublin
5 *
6 * Clustal-Omega is free software; you can redistribute it and/or
7 * modify it under the terms of the GNU General Public License as
8 * published by the Free Software Foundation; either version 2 of the
9 * License, or (at your option) any later version.
10 *
11 * This file is part of Clustal-Omega.
12 *
13 ********************************************************************/
14
15/*
16 * RCS $Id: pair_dist.h 302 2016-06-13 13:35:50Z fabian $
17 */
18
19
20#ifndef CLUSTALO_PAIR_DIST_H
21#define CLUSTALO_PAIR_DIST_H
22
23#define PAIRDIST_UNKNOWN 0
24/* k-tuple distances: Wilbur and Lipman (1983) */
25#define PAIRDIST_KTUPLE 1
26/* fractional identity between aligned sequences. denominator is
27 * minimum seq len (see squid:aligneval.c) */
28#define PAIRDIST_SQUIDID 2
29/* SQUIDID + Kimura correction */
30#define PAIRDIST_SQUIDID_KIMURA 3
31
32#include "seq.h"
33#include "symmatrix.h"
34
35extern int
36PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, bool bPercID,
37 const int istart, const unsigned long int iend,
38 const int jstart, const unsigned long int jend,
39 char *fdist_in, char *fdist_out);
40
41#endif
42
int PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, bool bPercID, const int istart, const unsigned long int iend, const int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out)
compute or read precomputed distances for given sequences
Definition pair_dist.c:277
structure for storing multiple sequences
Definition seq.h:47
symmetric matrix structure
Definition symmatrix.h:48